All free schools will be forced to present evolution as a comprehensive and central tenet of scientific theory, ministers have announced, following lobbying by senior scientists concerned that Christian-run institutions could exploit loopholes in the rules to present creationism as a credible theory.

The tightening of the funding rules for free schools comes after representations to the Department for Education by the Royal Society and its president, the Nobel-prizewinning geneticist Sir Paul Nurse, as well as by secular and humanist groups.

He said: "What they had done was only focus on part of the problem. They had, quite reasonably, controlled the possibility that creationism might be taught as science, but what hadn't been protected was that evolution should be taught at all.

"You could have ended up, if a school was so minded, not to teach creationism in science but to discuss creationism as the basis of the origin of species in religious studies, and not talk about evolution in science studies. In that case, the only message would have been about creationism and the message about evolution by natural selection could have been completely lost."

Nurse said he approached the DfE about the apparent "hole in the argument". He said: "To their credit they responded pretty rapidly.". The new clause in funding agreements says free schools must "make provision for the teaching of evolution as a comprehensive, coherent and extensively evidenced theory".

Lord Hill, the schools minister, wrote to Nurse this week to explain the change, saying: "While we have always been clear that we would expect to see evolution included in schools' science curricula, this new clause will provide more explicit reassurance that free schools will have to meet that expectation."

In a separate DfE statement, Hill said: "Free schools are being opened around the country in response to the demand from the local community for good school places. They are giving local parents more choice about where to send their child to school and help to raise standards in the area."

Nurse said he had broader worries about creationist groups operating schools. He said: "Talking personally, and not as president of the Royal Society, I have some concerns about that, but the major concern was this one and that has been dealt with by these new regulations."

Andrew Copson, head of the British Humanist Association, which was backed by Nurse in its Teach Evolution not Creationism campaign, welcomed the change as "an excellent additional safeguard". He said: "However, we continue to be concerned about the three free schools recently approved which are supportive of teaching creationism as science and which we must worry will continue to find ways to circumvent a ban in practice."

The new wording has been inserted into the agreement signed by Grindon Hall and will feature in any future agreements.